Updates

Model and report changes

  1. The model now accounts for the ongoing immunisation programme, stratifying the population of people still susceptible to infection with the virus according to their immunisation status (unimmunised/1 dose/2 doses). We use data on the daily proportions of the population getting immunised to inform this splitting of the population, assuming that it takes three weeks for vaccine-derived immunity to develop. Vaccine efficacy is assumed against both infection and death, using values for the efficacy in agreement with those found here. We have a changepoint in the vaccine efficacy on the 10th May, which marks a transition from alpha being the dominant variant, to delta.
  2. The model now also accounts for a different susceptibility to infection in each adult age group (no prior information is used); and for the under-15s, (using prior information from Viner et al, 2020, which estimates children to be less likely to acquire infection when in contact with an infectious individual).
  3. The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
  4. The geographical definition has been changed from the seven NHS regions (map) to the nine regions typically used in government (map). This new spatial definition more appropriately reflects the existing regional heterogeneity.
  5. The underlying probability of an unvaccinated individual dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) is allowed to change gradually over the course of 30 days every (approximately) 100 days. This is designed to reflect fluctuations due to seasonal effects, demand on healthcare services or the emergence of new virus variants of differing severity.
  6. The ‘Epidemic summary’ now only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme.

Updated findings

  1. The estimate of the daily number of new infections on the 17th August across England is 28,300 (24,000–33,600, 95% credible interval). The daily infection rate is estimated to be the highest in the East of England (EE) with 75 infections per 100K population per day. This corresponds to 4,660 new daily infections. The next highest rates of infection are in Yorkshire and Humber (YH) with 70 infections per 100K (3,820 daily infections). The East Midlands (EM), London (GL) and the South West (SW) all have over 50 new infections per 100k each day, with the North East over 40 per 100k. The North West (NW) is the region with the lowest incidence rate with 28 infections per 100K. Note that a substantial proportion of these daily infections will be asymptomatic.
  2. In contrast to the number of infections, the number of deaths occurring daily has increased and, for the 7th September we forecast between 38 and 79 deaths.
  3. The probability of Rt exceeding 1 has decreased in all regions. It is highest at 64% in the EE, close to 10% in GL, 6% in the SW, around 3% in YH, EM and SE and negligible or zero in the NW, WM and NE.
  4. The growth rate for England has decreased to -0.02 (-0.02–- -0.01) per day. This means that, nationally, the number of infections is highly likely to be decreasing, with a halving in the number of infections every 45 days. This pattern is common to the majority of regions.
  5. GL, followed by the NE and the WM, have the highest attack rates, that is the proportions of the regional populations who have ever been infected, with 37%, 36% and 32% respectively. The SW continues to have the lowest attack rate at 20%. These attack rates are consistent with our previous published report.
  6. Note that the deaths data used are only very weakly informative on Rt over the last two weeks and are thankfully sparse. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

The plots of the estimated Rt over the most recent weeks show the Rt following a declining trend from peaks of around 1.50 to a plateau just below 1. This downward trend in Rt from the peak is still largely driven by the indices of mobility, and particularly by the recent school holiday.

The incidence of deaths has been gradually increasing since mid June, although the actual numbers remain low in comparison to the peaks of the first two waves of infection. In line with our previous publication, our projections for the number of deaths suggest that we are now at, or close to, the peak of the current summer wave.

Plots of the IFR over time show that from the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop indicates the benefits of immunisation against death over and above the benefits against infection. Specifically, there is an estimated fall to a still-high 2.5% (2.4%–2.7%) in the over-75s and 0.12% (0.12%–0.13%) overall in mid-July. The overall impact of the immunisation programme can be seen more clearly in the ‘All Ages’ plot, where the precipitous decline in IFR since late January is a product of this efficacy against death but also of the increasing proportion of infections in young people; older age groups are immunised and become more protected against infection. There is an initial suggestion that the IFR may have risen slightly over the last month, and this is to be monitored.

For context, alongside the data used here, reported new positive tests have shown a very gradual increasing trend over the last couple of weeks. This trend is highly dependent on the targeting of testing and the public’s testing behaviour and, therefore, is difficult to interpret. However, a downturn in hospital admissions has plateaued, subject to some regional variation. Prevalence of infection, as estimated by the ONS Coronavirus Infections Survey, remains high, staying constant at around 1.30% in England, having declined from around 1.5% in mid-to-late July.

Summary

Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.

Methods

We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.

Data sources

We use:

  1. Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
    • the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
    • NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
    • Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
  2. Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.

Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).

  1. Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
  2. Information on contacts between different age groups from:
    • A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
    • Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
    • The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
    • Data from the Department for Education describing the proportion of children currently attending school.
  3. Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.

Epidemic summary

Current \(R_t\)

Value of \(R_t\), the average number of secondary infections due to a typical infection today.

Number of infections

Attack rate

The percentage of a given group that has been infected.

By region

By age

Current IFR

Change in infections incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England -0.02 -0.02 -0.01
East of England 0.00 -0.02 0.02
East Midlands -0.02 -0.05 0.00
London -0.01 -0.03 0.01
North East -0.05 -0.08 -0.03
North West -0.03 -0.05 0.00
South East -0.02 -0.04 0.00
South West -0.02 -0.04 0.01
West Midlands -0.04 -0.07 -0.02
Yorkshire and The Humber -0.02 -0.04 0.00

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 45.09 28.94 116.32
East of England NA 44.28 NA
East Midlands 27.94 14.52 NA
London 59.87 22.12 NA
North East 13.63 8.61 25.39
North West 24.40 12.68 189.92
South East 34.52 17.34 2465.60
South West 38.41 16.87 NA
West Midlands 15.56 9.50 32.60
Yorkshire and The Humber 37.73 18.36 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA NA NA
East of England 206.76 30.54 NA
East Midlands NA 23559.11 NA
London NA 125.76 NA
North East NA NA NA
North West NA NA NA
South East NA NA NA
South West NA 125.32 NA
West Midlands NA NA NA
Yorkshire and The Humber NA 3409.42 NA

Change in deaths incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England 0.00 -0.01 0.01
East of England 0.02 0.00 0.04
East Midlands 0.00 -0.02 0.01
London 0.00 -0.01 0.02
North East -0.02 -0.03 -0.01
North West -0.01 -0.02 0.01
South East 0.00 -0.01 0.02
South West 0.00 -0.01 0.02
West Midlands -0.02 -0.03 0.00
Yorkshire and The Humber 0.00 -0.01 0.02

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 1308.73 104.23 NA
East of England NA NA NA
East Midlands 178.64 37.98 NA
London NA 72.91 NA
North East 32.34 20.08 114.31
North West 70.15 27.90 NA
South East NA 56.81 NA
South West NA 46.65 NA
West Midlands 39.56 22.76 201.31
Yorkshire and The Humber NA 73.96 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA 120.31 NA
East of England 40.35 19.72 433.45
East Midlands NA 56.14 NA
London 194.49 40.72 NA
North East NA NA NA
North West NA 91.63 NA
South East 589.66 43.50 NA
South West 737.03 37.21 NA
West Midlands NA NA NA
Yorkshire and The Humber 185.23 38.09 NA

Infections and deaths

The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (17 Aug).

Infection incidence

By region

By age

Cumulative infections

By region

By age

Deaths incidence

By region

By age

Cumulative deaths

By region

By age

IFR

Prob \(R_t > 1\)

The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.

\(R_t\)

Copyright © MRC Biostatistics Unit, University of Cambridge